User: Vitis

gravatar for Vitis
Vitis2.4k
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New York
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9 years, 8 months ago
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 333 results • page 1 of 34 • next >
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Comment: C: Gene expression heatmap following pseudotime analysis
... I updated my original question with an example plot. ...
written 5 days ago by Vitis2.4k
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Gene expression heatmap following pseudotime analysis
... Going through some of the instructions and tutorials for single cell mRNA-Seq analysis, I was looking for some solid and good looking gene expression heatmap plotting following pseudotime, where the gradual shift of transient expression could be clearly shown. Since monocle3 retired the plot_pseudot ...
rna-seq written 5 days ago by Vitis2.4k
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Comment: C: GATK GenomicsDBImport intervals
... I remember at one time GATK GenomicsDBImport did not allow multiple intervals. It seems now this problem has been fixed. See: https://gatkforums.broadinstitute.org/gatk/discussion/13447/genomicsdbimport-intervals. Can you check your GATK version? ...
written 8 months ago by Vitis2.4k
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Comment: C: Analysis of host-parasite mixed transcriptome
... Great! Thanks! If you put this in as an answer, I'll click "accept". ...
written 8 months ago by Vitis2.4k
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Analysis of host-parasite mixed transcriptome
... I am wondering what the best practices are analyzing host-parasite mixed transcriptomes. If I have mRNA-Seq data from infected host tissues that contain both host and parasite genomes, which would be the best way to tease them apart? Mapping to a combined reference (host + parasite), or mapping to t ...
alignment rna-seq written 8 months ago by Vitis2.4k • updated 8 months ago by GenoMax96k
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Variant calling from short/long read hybrid BAM
... Is there an approach that takes in a hybrid BAM that contains both short and long reads and call variants, especially bigger structural variants? I think it will be more common to have both long and short reads for a genomic region. A variant caller that takes advantage of the hybrid data may be val ...
snp sequencing written 11 months ago by Vitis2.4k
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Answer: A: Circos Plot for synteny file
... On way to do this is to lay out the chromosomes from two genomes into left and right panels, then draw connections/links based on synteny relationships between chromosomes across genomes. See Fig. 2 from the Canola genome paper published in 2014. https://science.sciencemag.org/content/345/6199/950 ...
written 14 months ago by Vitis2.4k
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Answer: A: How are haplotypes/heterozygosity resolved in sequence assembly?
... I think the ultimate goal for assembling a heterozygous genome is to fully resolve the two haplotypes, essentially two genome assemblies. Platanus seems to be doing a fairly job dealing with heterozygous genomes. Also, long-read sequencing technologies like Nanopore and PacBio would enable variant p ...
written 14 months ago by Vitis2.4k
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Answer: A: A good tutorial for eukaryotic phylogeny?
... I came across this paper recently about reconstruction of genome phylogeny for a butterfly species radiation. The methodology might be interesting for you to take a look. They used long reads assembled genomic sequences and Cactus to align the genomes, then created gene trees and species trees, etc. ...
written 14 months ago by Vitis2.4k
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Answer: A: BWA Mem -M flag (mark split hits) effect on structural variation calling
... I've never used -M option for structural variant calling. Based on this BWA thread, you may lose supplementary mapping information by using -M option, because -M may label split reads as duplicates and strip the secondary/supplementary mapping information. I believe at least some SV tools use split ...
written 15 months ago by Vitis2.4k

Latest awards to Vitis

Popular Question 9 months ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 14 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Voter 15 months ago, voted more than 100 times.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 23 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 23 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 2.2 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 4.1 years ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 4.1 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 6.7 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Autobiographer 6.9 years ago, has more than 80 characters in the information field of the user's profile.

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